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James Taylor
52 lines
1.6 KiB
Python
52 lines
1.6 KiB
Python
from galaxy.test.base.twilltestcase import TwillTestCase
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#from twilltestcase import TwillTestCase
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class UcscTests(TwillTestCase):
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def test_00_first(self): # will run first due to its name
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"""3A_GetData: Clearing history"""
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self.clear_history()
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def test_10_upload(self):
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"""3A_GetData: Testing single upload"""
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self.clear_history()
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self.upload_file('MyData.bed')
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self.check_data('MyData.bed', hid=1)
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def test_20_UCSC_bed(self):
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"""3A_GetData: Getting bed files from UCSC"""
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self.clear_history()
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self.run_tool('ucsc_proxy')
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params = dict(
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hgta_regionType="range",
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hgta_outputType="bed",
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)
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self.submit_form(1, button="hgta_doTopSubmit", **params)
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self.submit_form(1, button="hgta_doGetBed" )
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self.wait()
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self.check_data('3A_GetData_ucsc_bed_range.dat', hid=1)
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def test_30_Biomart_Uniprot(self):
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"""3A_GetData: Connection to Biomart"""
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# some button indices are hardcoded (twill limitation)
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self.run_tool('biomart')
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self.submit_form(form='settings', button='stage_filter',
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database='UNIPROTPROTOTYPE4-5(EBI)__default', dataset='uniprot'
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)
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self.submit_form(form='settings', button=6,
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uniprot_collection_start=1, uniprot_collection_end=1,
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uniprot_component_start=1000, uniprot_component_end=2000
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)
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#self.submit_form(form='settings', button=5,
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# outtype='Features', outformat='tsv'
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#)
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#self.check_data('biomart_uniprot.dat')
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